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Package 322/419HostnameOS / ArchBUILDCHECKBUILD BIN
R453Plus1Toolbox 1.0.1
H-U Klein
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/R453Plus1Toolbox
Last Changed Rev: 50365 / Revision: 54281
Last Changed Date: 2010-10-20 09:22:14 -0700 (Wed, 20 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: R453Plus1Toolbox
Version: 1.0.1
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings R453Plus1Toolbox_1.0.1.tar.gz
StartedAt: 2011-03-31 07:52:25 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 07:56:27 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 242.3 seconds
RetCode: 0
Status:  OK  
CheckDir: R453Plus1Toolbox.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/R453Plus1Toolbox.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'R453Plus1Toolbox/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'R453Plus1Toolbox' version '1.0.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'R453Plus1Toolbox' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getMutations: no visible binding for global variable 'PatternStart'
.getMutations: no visible binding for global variable 'PatternEnd'
.htmlReport: no visible binding for global variable 'VarFreqForward'
.htmlReport: no visible binding for global variable 'VarFreqReverse'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

R453Plus1Toolbox.Rcheck/00install.out:

* installing *source* package 'R453Plus1Toolbox' ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:Biobase':

    updateObject

The following object(s) are masked from 'package:base':

    Map, cbind, eval, mapply, order, paste, pmax, pmax.int, pmin,
    pmin.int, rbind, rep.int, table

Loading required package: BSgenome
Loading required package: GenomicRanges
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (R453Plus1Toolbox)

R453Plus1Toolbox.Rcheck/R453Plus1Toolbox-Ex.timings:

nameusersystemelapsed
AVASet-class0.290.000.30
AVASet0.040.000.03
AnnotatedVariants-class000
MapperSet-class0.070.000.08
MapperSet0.020.000.01
alignShortReads0.950.001.05
annotateVariants000
assayDataAmp0.020.000.02
avaSetExample0.030.000.03
avaSetFiltered0.060.000.06
avaSetFiltered_annot000
breakpoints0.020.000.02
captureArray000
coverageOnTarget0.860.000.98
demultiplexReads0.310.000.36
detectBreakpoints0.790.000.88
fDataAmp0.030.010.05
featureDataAmp0.030.000.03
filterChimericReads1.750.001.81
genomeSequencerMIDs0.050.000.05
getAlignedReads0.190.000.18
getVariantPercentages0.070.000.06
htmlReport5.010.285.61
mapperSetExample0.020.000.02
mergeBreakpoints8.370.158.67
plotAmpliconCoverage000
plotChimericReads5.410.015.44
plotVariants000
plotVariationFrequency000
readsOnTarget0.50.00.5
referenceSequences0.020.000.01
removeLinker0.030.000.03
sequenceCaptureLinkers0.010.000.02
setVariantFilter0.130.000.12
transcriptdf000